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E-learning recommendation framework based on deep learning

Published in 2017 IEEE international conference on systems, man, and cybernetics (SMC), 2017

Recommended citation: Wang, X., Zhang, Y., Yu, S., Liu, X., Yuan, Y., & Wang, F. Y. (2017, October). E-learning recommendation framework based on deep learning. In 2017 IEEE international conference on systems, man, and cybernetics (SMC) (pp. 455-460). IEEE. https://ieeexplore.ieee.org/abstract/document/8122647?casa_token=zEmxWnuthkwAAAAA:bR9DtfG1-FLTIMfaEe5RJahJw7qUgB2G8dB0Y_1jWFxZJUOuXXbg6gZXRsAAyhVNg2Im7luSBQ

Computerized adaptive English ability assessment based on deep learning

Published in Image and Video Technology: PSIVT 2017 International Workshops, 2017

Recommended citation: Wang, X., Zhang, Y., Yu, S., Liu, X., & Wang, F. Y. (2018). Computerized adaptive English ability assessment based on deep learning. In Image and Video Technology: PSIVT 2017 International Workshops, Wuhan, China, November 20-24, 2017, Revised Selected Papers 8 (pp. 158-171). Springer International Publishing. https://link.springer.com/chapter/10.1007/978-3-319-92753-4_13

Impact of AlphaFold on structure prediction of protein complexes: the CASP15‐CAPRI experiment

Published in Proteins: Structure, Function, and Bioinformatics, 2023

Recommended citation: Lensink, M. F., ..., Zhang, Y,... & Wodak, S. J. (2023). Impact of AlphaFold on structure prediction of protein complexes: the CASP15‐CAPRI experiment. Proteins: Structure, Function, and Bioinformatics, 91(12), 1658-1683. https://onlinelibrary.wiley.com/doi/full/10.1002/prot.26609

Distance-AF: Modifying Predicted Protein Structure Models by Alphafold2 with User-Specified Distance Constraints

Published in BioRxiv, 2023

Recommended citation: Zhang, Y., Zhang, Z., Kagaya, Y., Terashi, G., Zhao, B., Xiong, Y., & Kihara, D. (2023). Distance-AF: Modifying Predicted Protein Structure Models by Alphafold2 with User-Specified Distance Constraints. bioRxiv, 2023-12. https://www.biorxiv.org/content/10.1101/2023.12.01.569498v1

Retrieval-reasoning large language model-based synthetic clinical trial generation

Published in Arxiv, 2024

Recommended citation: Xu, Zerui, Fang Wu, Yuanyuan Zhang, and Yue Zhao. "Retrieval-reasoning large language model-based synthetic clinical trial generation." arXiv preprint arXiv:2410.12476 (2024). https://arxiv.org/pdf/2410.12476?

A generalizable Hi-C foundation model for chromatin architecture, single-cell and multi-omics analysis across species

Published in BioRxiv, 2024

Recommended citation: Xiao Wang, Yuanyuan Zhang, Suhita Ray, Anupama Jha, Tangqi Fang, Shengqi Hang, Sergei Doulatov, William Stafford Noble, & Sheng Wang. A generalizable Hi-C foundation model for chromatin architecture, single-cell and multi-omics analysis across species. bioRxiv, 2024. https://www.biorxiv.org/content/10.1101/2024.12.16.628821v1.full

CryoNeRF: reconstruction of homogeneous and heterogeneous cryo-EM structures using neural radiance field

Published in BioRxiv, 2025

Recommended citation: Qu, Huaizhi, Xiao Wang, Yuanyuan Zhang, Sheng Wang, William Stafford Noble, and Tianlong Chen. "CryoNeRF: reconstruction of homogeneous and heterogeneous cryo-EM structures using neural radiance field." bioRxiv (2025): 2025-01. https://www.biorxiv.org/content/10.1101/2025.01.10.632460v1.full.pdf

Biomedical foundation model: A survey

Published in Arxiv, 2025

Recommended citation: Liu, Xiangrui, Yuanyuan Zhang, Yingzhou Lu, Changchang Yin, Xiaoling Hu, Xiaoou Liu, Lulu Chen et al. "Biomedical foundation model: A survey." arXiv preprint arXiv:2503.02104 (2025). https://arxiv.org/pdf/2503.02104

PoseX: AI Defeats Physics Approaches on Protein-Ligand Cross Docking

Published in Arxiv, 2025

Recommended citation: Jiang, Yize, Xinze Li, Yuanyuan Zhang, Jin Han, Youjun Xu, Ayush Pandit, Zaixi Zhang et al. "PoseX: AI Defeats Physics Approaches on Protein-Ligand Cross Docking." arXiv preprint arXiv:2505.01700 (2025). https://arxiv.org/pdf/2505.01700

Distance-AF: Flexible protein structure prediction with distance constraints using AlphaFold2

Published: May 17, 2023

Distance-AF: Flexible protein structure prediction with distance constraints using AlphaFold2

Published: April 04, 2024

CS38003-Python Programming

Undergraduate course, Department of Computer Science, Purdue University, 2021

CS49000-DSC:Data Science Capstone

Undergraduate course, Department of Computer Science, Purdue University, 2021

CS50023-Data Engineering I

Graduate course, Department of Computer Science, Purdue University, 2022

CS25100-Data Structures And Algorithms

Undergraduate course, Department of Computer Science, Purdue University, 2023